File:  [mozdev] / biobar / www / customize.html
Revision 1.1: download - view: text, annotated - select for diffs - revision graph
Wed Mar 9 16:48:51 2005 UTC (14 years, 7 months ago) by jawahar
Branches: MAIN
CVS tags: HEAD
added customize instructions

    1: <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
    2: <html>
    3: <head>
    4:   <meta content="text/html; charset=ISO-8859-1"
    5:  http-equiv="content-type">
    6:   <title>Customizing biobar search menus</title>
    7: </head>
    8: <body>
    9: <div style="text-align: center;">
   10: <h2><span style="font-weight: bold;">Customize your search menu</span></h2>
   11: <div style="text-align: justify;"><span style="font-weight: bold;"><span
   12:  style="font-weight: bold;"></span></span>
   13: <p><span style="font-weight: bold;"><span style="font-weight: bold;"><span
   14:  style="font-weight: bold;"></span></span></span>With version 1.3 of
   15: biobar it is possible to customize the search menu of the toolbar. The
   16: procedure involves editing an XML file and saving the file in your
   17: profile directory.</p>
   18: <br>
   19: There are two files which can be edited to add additional search
   20: terms/menu's to your searches.<br>
   21: <br>
   22: <ol>
   23:   <li>BiobarSearch.xml - Provides the menu listing and URLs for
   24: producing the standard search menu (individual databases).</li>
   25:   <li>BiobarGroups.xml - Provides the URLs and menu for 'Searching by
   26: Groups'&nbsp; option, which can be chosen from options.</li>
   27: </ol>
   28: <p>Before customizing the search menu, please copy these files to from
   29: the following links to your profile directory. Following these links
   30: will open up the XML file on your browser, please choose File-&gt; Save
   31: Page As to save the files. <span style="font-style: italic;">Please do
   32: not rename these files !!</span></p>
   33: <ul>
   34:   <li><a href="http://biobar.mozdev.org/BiobarSearch.xml">BiobarSearch.xml</a></li>
   35:   <li><a href="http://biobar.mozdev.org/BiobarGroups.xml">BiobarGroups.xml</a></li>
   36: </ul>
   37: Copy these files over to your Profile Directory. <br>
   38: <br>
   39: <span style="font-weight: bold;">Locating your Profile Directory: </span>From
   40: the main browser toolbar, choose Tools -&gt; Biobar -&gt; My Profile
   41: Directory.<span style="font-weight: bold;"> </span>The information
   42: will be displayed to you in an alert box.<br>
   43: <br>
   44: <span style="font-weight: bold;">Editing BiobarSearch.xml: </span><br>
   45: <br>
   46: Go to your profile directory using the paths above. Open the xml file
   47: in yoru favorite editor. This file has the following syntax:<br>
   48: <br>
   49: <span style="font-weight: bold;"><span style="font-weight: bold;"><span
   50:  style="font-weight: bold;"></span></span></span>
   51: <pre>&lt;?xml version="1.0"?&gt;<br>&lt;biobar&gt;<br>       &lt;Databases&gt;<br>---<br>---<br>               &lt;Group type="Fungal"&gt;<br>                        &lt;Database type="SGD"&gt;<br>                                &lt;Menuitem name="QuickSearch" url="Some Search URL"/&gt;<br>				&lt;Menuitem name-"...." url="....."/&gt;<br>                        &lt;/Database&gt;<br>                &lt;/Group&gt;<br>        &lt;/Databases&gt;<br>&lt;/biobar&gt;<br><br></pre>
   52: The Group definition indicates the main groups of search databases in
   53: the search menu. EBI, NCBI, Plant, Animal, Structure etc. Please add a
   54: group of your own and give it a unique name like &lt;Group type="my
   55: menu"&gt;. Inside each group are databases each having a name. For
   56: example, under structure, we have databases like MSD, RCSB etc. Add
   57: your database under your group like &lt;Database type="MyDatabase"&gt;.
   58: Under each Database are a set of searchterms you would like to search
   59: by followed by the URL leading upto the search.<br>
   60: <br>
   61: For example if you want to search by Group (My Menu) having a database
   62: (MyDatabase) which has a searchitem and url, you would edit the XML
   63: file and add at the following:<br>
   64: <br>
   65: <pre>&lt;Group type="My Menu"&gt;<br>&lt;Database type="MyDatabase"&gt;<span
   66:  style="font-family: monospace;"></span><br>&lt;Menuitem name="Keyword" url="http://mydatabase.org/something.cgi?something=something&amp;amp;keyword="/&gt;<br>&lt;/Database&gt;<br>&lt;/Group&gt;<br><br></pre>
   67: <p>Where the the url is everything but the text you will actually
   68: search. Please note that each menuitem is terminated with a /. Please
   69: also note the format for ampersand. The items you add should be nested
   70: within the overall XML tree. Ideally you would add a new &lt;Group&gt;
   71: below a &lt;/Group&gt;.<br>
   72: </p>
   73: <p>Please save the XML file in your profile directory. Check to see
   74: that the XML file is valid by opening this XML file in your browser. If
   75: it renders properly as a tree, then you have a valid XML. Else please
   76: correct the errors. </p>
   77: <p>Once you have saved the XML file, restart
   78: your browser, and
   79: the new search menu containing the search database you added will show
   80: up in the Search Window. You will also be able to choose the new
   81: database/s as a default from the options window.<br>
   82: </p>
   83: <p><span style="font-weight: bold;">Editing BiobarGroups.xml: </span><br>
   84: </p>
   85: <p>Save BiobarGroups.xml in your profile directory as described above.
   86: Open this file for editing your favorite browser. This file has a
   87: format similar to that showb below:<br>
   88: </p>
   89: <pre>&lt;?xml version="1.0"?&gt;<br>&lt;biobarGroups&gt;<br>        &lt;Group name="Structures"&gt;<br>                &lt;Menuitems&gt;<br>                        &lt;Menuitem SearchTerm="PDB ID"&gt;<br>                                &lt;url&gt;http://www.ebi.ac.uk/msd-srv/atlas?toolbar=biobar&amp;amp;id=&lt;/url&gt;<br>                                &lt;url&gt;http://oca.ebi.ac.uk/oca-bin/ocaids?toolbar=biobar&amp;amp;id=&lt;/url&gt;<br>                                &lt;url&gt;http://www.rcsb.org/pdb/cgi/explore.cgi?toolbar=biobar&amp;amp;pdbId=&lt;/url&gt;<br>                                &lt;url&gt;http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?toolbar=biobar&amp;amp;pdbcode=&lt;/url&gt;<br>                        &lt;/Menuitem&gt;<br>		&lt;/Menuitems&gt;<br>	&lt;/Group&gt;<br>&lt;/biobarGroups&gt;<br><br></pre>
   90: Each Group described a search Type (Structures, Function, Taxonomy
   91: etc). Each search Type has a set of searchTerms associated with the
   92: searchType. For example, one could search all structrual databases for
   93: PDB code, keyword, author etc. For each searchTerm, there are a set of
   94: URLs which describe the full command needed for searching.<br>
   95: <br>
   96: <p>If you wanted to add your own searchType (say Sequences) containing
   97: searchTerms Author, Keyword etc, you would have to add a new Group with
   98: a tree like:</p>
   99: <br>
  100: <br>
  101: <pre>&lt;Group name="Sequences"&gt;<br>	&lt;Menuitems&gt;<br>		&lt;Menuitem SearchTerm="Keyword"&gt;<br>			&lt;url&gt;SomeURL containing the whole path&lt;/url&gt;<br>			&lt;url&gt;&lt;/url&gt;<br>		&lt;/Menuitem&gt;<br>		&lt;Menuitem SearchTerm+"Author"&gt;<br>			&lt;url&gt;&lt;/url&gt;<br>			&lt;url&gt;&lt;/url&gt;<br>		&lt;/Menuitem&gt;<br>	&lt;/Menuitems&gt;<br>&lt;/Group&gt;<br><br></pre>
  102: <p>Once you have made the changes, save the file as BiobarGroups.xml in
  103: your profile area. Check that the XML file is valid by opening the file
  104: in your browser. Restart your browser. If you chose the 'Search Groups'
  105: in the biobar options window, then your database will show up.</p>
  106: <br>
  107: </div>
  108: </div>
  109: </body>
  110: </html>

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